%CAR+ cells between responders in IP and PBMC
Results
IP
CD4 + CD8
## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df)
##
## n= 19, number of events= 5
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos 0.0939 1.0984 4.2036 0.022 0.982
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 1.098 0.9104 0.0002902 4158
##
## Concordance= 0.516 (se = 0.128 )
## Likelihood ratio test= 0 on 1 df, p=1
## Wald test = 0 on 1 df, p=1
## Score (logrank) test = 0 on 1 df, p=1## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "ALL"))
##
## n= 7, number of events= 1
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos -2.2279 0.1078 10.6122 -0.21 0.834
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 0.1078 9.28 0.00000000009984 116297268
##
## Concordance= 0.5 (se = 0.204 )
## Likelihood ratio test= 0.05 on 1 df, p=0.8
## Wald test = 0.04 on 1 df, p=0.8
## Score (logrank) test = 0.04 on 1 df, p=0.8## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "MCL"))
##
## n= 12, number of events= 4
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos 0.3104 1.3640 5.5422 0.056 0.955
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 1.364 0.7331 0.00002614 71172
##
## Concordance= 0.533 (se = 0.131 )
## Likelihood ratio test= 0 on 1 df, p=1
## Wald test = 0 on 1 df, p=1
## Score (logrank) test = 0 on 1 df, p=1CD4 / CD8
## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(major_type == "CD4"))
##
## n= 19, number of events= 5
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos 0.8966 2.4512 4.3946 0.204 0.838
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 2.451 0.408 0.0004453 13493
##
## Concordance= 0.5 (se = 0.124 )
## Likelihood ratio test= 0.04 on 1 df, p=0.8
## Wald test = 0.04 on 1 df, p=0.8
## Score (logrank) test = 0.04 on 1 df, p=0.8## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "ALL" & major_type == "CD4"))
##
## n= 7, number of events= 1
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos -4.66386 0.00943 13.64732 -0.342 0.733
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 0.00943 106 0.0000000000000228 3900626164
##
## Concordance= 0.5 (se = 0.204 )
## Likelihood ratio test= 0.14 on 1 df, p=0.7
## Wald test = 0.12 on 1 df, p=0.7
## Score (logrank) test = 0.12 on 1 df, p=0.7## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "MCL" & major_type == "CD4"))
##
## n= 12, number of events= 4
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos 2.269 9.669 6.029 0.376 0.707
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 9.669 0.1034 0.00007142 1309098
##
## Concordance= 0.5 (se = 0.16 )
## Likelihood ratio test= 0.15 on 1 df, p=0.7
## Wald test = 0.14 on 1 df, p=0.7
## Score (logrank) test = 0.14 on 1 df, p=0.7## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(major_type == "CD8"))
##
## n= 19, number of events= 5
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos 1.498 4.472 4.475 0.335 0.738
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 4.472 0.2236 0.0006942 28811
##
## Concordance= 0.562 (se = 0.121 )
## Likelihood ratio test= 0.12 on 1 df, p=0.7
## Wald test = 0.11 on 1 df, p=0.7
## Score (logrank) test = 0.11 on 1 df, p=0.7## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "ALL" & major_type == "CD8"))
##
## n= 7, number of events= 1
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos 4.390 80.629 9.697 0.453 0.651
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 80.63 0.0124 0.000000449 14477814934
##
## Concordance= 0.833 (se = 0.152 )
## Likelihood ratio test= 0.21 on 1 df, p=0.6
## Wald test = 0.2 on 1 df, p=0.7
## Score (logrank) test = 0.21 on 1 df, p=0.6## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "MCL" & major_type == "CD8"))
##
## n= 12, number of events= 4
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos 0.2183 1.2439 5.6173 0.039 0.969
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 1.244 0.8039 0.00002057 75212
##
## Concordance= 0.5 (se = 0.163 )
## Likelihood ratio test= 0 on 1 df, p=1
## Wald test = 0 on 1 df, p=1
## Score (logrank) test = 0 on 1 df, p=1Correlates to %CAR+ cells
CD4 + CD8
CD4 / CD8
CD4
CD8
PBMC
CD4 + CD8
## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df)
##
## n= 20, number of events= 5
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos -5.139027 0.005863 2.256915 -2.277 0.0228 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 0.005863 170.5 0.00007032 0.4889
##
## Concordance= 0.882 (se = 0.075 )
## Likelihood ratio test= 5.61 on 1 df, p=0.02
## Wald test = 5.18 on 1 df, p=0.02
## Score (logrank) test = 5.77 on 1 df, p=0.02## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "ALL"))
##
## n= 8, number of events= 1
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos -11.668238547 0.000008561 16.393660278 -0.712 0.477
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 0.000008561 116802 0.00000000000000000009511 770650231
##
## Concordance= 0.857 (se = 0.132 )
## Likelihood ratio test= 2.51 on 1 df, p=0.1
## Wald test = 0.51 on 1 df, p=0.5
## Score (logrank) test = 2.22 on 1 df, p=0.1## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "MCL"))
##
## n= 12, number of events= 4
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos -10.74449210 0.00002156 6.42173114 -1.673 0.0943 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 0.00002156 46374 0.00000000007371 6.308
##
## Concordance= 0.867 (se = 0.104 )
## Likelihood ratio test= 6.98 on 1 df, p=0.008
## Wald test = 2.8 on 1 df, p=0.09
## Score (logrank) test = 5.77 on 1 df, p=0.02
CD4 / CD8
## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(major_type == "CD4"))
##
## n= 20, number of events= 5
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos -6.76802 0.00115 2.89422 -2.338 0.0194 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 0.00115 869.6 0.000003955 0.3344
##
## Concordance= 0.868 (se = 0.087 )
## Likelihood ratio test= 7.98 on 1 df, p=0.005
## Wald test = 5.47 on 1 df, p=0.02
## Score (logrank) test = 7.36 on 1 df, p=0.007## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "ALL" & major_type == "CD4"))
##
## n= 8, number of events= 1
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos -14.6460505776 0.0000004358 18.9859176817 -0.771 0.44
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 0.0000004358 2294558 0.00000000000000000000003009 6311658350
##
## Concordance= 0.857 (se = 0.132 )
## Likelihood ratio test= 2.38 on 1 df, p=0.1
## Wald test = 0.6 on 1 df, p=0.4
## Score (logrank) test = 1.52 on 1 df, p=0.2## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "MCL" & major_type == "CD4"))
##
## n= 12, number of events= 4
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos -11.0368264 0.0000161 6.9995323 -1.577 0.115
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 0.0000161 62120 0.00000000001773 14.61
##
## Concordance= 0.933 (se = 0.067 )
## Likelihood ratio test= 8.58 on 1 df, p=0.003
## Wald test = 2.49 on 1 df, p=0.1
## Score (logrank) test = 7.87 on 1 df, p=0.005## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(major_type == "CD8"))
##
## n= 18, number of events= 4
## (1 observation deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos -2.69303 0.06768 2.17902 -1.236 0.216
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 0.06768 14.78 0.0009455 4.844
##
## Concordance= 0.787 (se = 0.108 )
## Likelihood ratio test= 1.56 on 1 df, p=0.2
## Wald test = 1.53 on 1 df, p=0.2
## Score (logrank) test = 1.57 on 1 df, p=0.2## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "ALL" & major_type == "CD8"))
##
## n= 7, number of events= 0
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos NA NA 0 NA NA
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos NA NA NA NA
##
## Concordance= NA (se = NA )
## Likelihood ratio test= 0 on 0 df, p=1
## Wald test = 0 on 0 df, p=1
## Score (logrank) test = 0 on 0 df, p=1## Call:
## coxph(formula = Surv(PFS_days, PFS) ~ percCarPos, data = df %>%
## filter(disease == "MCL" & major_type == "CD8"))
##
## n= 11, number of events= 4
##
## coef exp(coef) se(coef) z Pr(>|z|)
## percCarPos -20.292980742951 0.000000001538 10.902066416320 -1.861 0.0627 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## percCarPos 0.000000001538 650323665 0.0000000000000000008073 2.929
##
## Concordance= 0.963 (se = 0.04 )
## Likelihood ratio test= 9.76 on 1 df, p=0.002
## Wald test = 3.46 on 1 df, p=0.06
## Score (logrank) test = 5.98 on 1 df, p=0.01
Correlates to %CAR+ cells
CD4 + CD8
CD4 / CD8
CD4
## Warning: Removed 4 rows containing missing values or values outside the scale range
## (`geom_smooth()`).
CD8
## Warning: Removed 52 rows containing non-finite outside the scale range
## (`stat_smooth()`).## Warning: Removed 52 rows containing non-finite outside the scale range
## (`stat_cor()`).## Warning: Removed 52 rows containing missing values or values outside the scale range
## (`geom_point()`).
